8Y18
Cryo-EM structure of SARS-CoV-2 Omicron JN.1 RBD in complex with human ACE2 (local refinement from the spike protein)
Entity
Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
1 | A (A) | Angiotensin-converting enzyme 2 | polymer | 603 | 69982.6 | 1 | UniProt (Q9BYF1) Pfam (PF01401) | Homo sapiens (human) | ACE-related carboxypeptidase,Angiotensin-converting enzyme homolog,ACEH,Metalloprotease MPROT15 |
2 | B (B) | Spike glycoprotein | polymer | 1248 | 138697.1 | 1 | UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601) | Severe acute respiratory syndrome coronavirus 2 (2019-nCoV SARS-CoV-2) | S glycoprotein,E2,Peplomer protein |
3 | C, D (C, D) | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 586.5 | 2 | In PDB GlyTouCan (G15407YE) | |||
4 | E, F, G (E, F, G) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 3 | In PDB GlyTouCan (G42666HT) | |||
5 | H (A) | ZINC ION | non-polymer | 65.4 | 1 | Chemie (ZN) | |||
6 | I, J, K (A, B) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 3 | Chemie (NAG) |
Sequence modifications
A: 19 - 615 (UniProt: Q9BYF1)
B: 4 - 1208 (UniProt: P0DTC2)
PDB | External Database | Details |
---|---|---|
His 616 | - | expression tag |
His 617 | - | expression tag |
His 618 | - | expression tag |
His 619 | - | expression tag |
His 620 | - | expression tag |
His 621 | - | expression tag |
PDB | External Database | Details |
---|---|---|
Met 20 | - | insertion |
Pro 21 | Asn 17 | variant |
Phe 23 | Thr 19 | variant |
Asn 24 | Thr 20 | variant |
Leu 25 | Arg 21 | variant |
Ile 26 | Thr 22 | variant |
Thr 27 | Gln 23 | variant |
Thr 28 | Leu 24 | variant |
Thr 29 | Pro 25 | variant |
Gln 30 | Pro 26 | variant |
Ser 31 | Ala 27 | variant |
Leu 54 | Ser 50 | variant |
- | His 69 | deletion |
- | Val 70 | deletion |
Phe 129 | Val 127 | variant |
Asp 144 | Gly 142 | variant |
- | Tyr 144 | deletion |
Ser 158 | Phe 157 | variant |
Gly 159 | Arg 158 | variant |
- | Asn 211 | deletion |
Ile 212 | Leu 212 | variant |
Gly 213 | Val 213 | variant |
Phe 216 | Leu 216 | variant |
Asn 245 | His 245 | variant |
Asp 264 | Ala 264 | variant |
Val 332 | Ile 332 | variant |
His 339 | Gly 339 | variant |
Thr 356 | Lys 356 | variant |
Phe 371 | Ser 371 | variant |
Pro 373 | Ser 373 | variant |
Phe 375 | Ser 375 | variant |
Ala 376 | Thr 376 | variant |
Lys 403 | Arg 403 | variant |
Asn 405 | Asp 405 | variant |
Ser 408 | Arg 408 | variant |
Asn 417 | Lys 417 | variant |
Lys 440 | Asn 440 | variant |
His 445 | Val 445 | variant |
Ser 446 | Gly 446 | variant |
Asp 450 | Asn 450 | variant |
Trp 452 | Leu 452 | variant |
Ser 455 | Leu 455 | variant |
Lys 460 | Asn 460 | variant |
Asn 477 | Ser 477 | variant |
Lys 478 | Thr 478 | variant |
Lys 481 | Asn 481 | variant |
- | Val 483 | deletion |
Lys 484 | Glu 484 | variant |
Pro 486 | Phe 486 | variant |
Arg 498 | Gln 498 | variant |
Tyr 501 | Asn 501 | variant |
His 505 | Tyr 505 | variant |
Lys 554 | Glu 554 | variant |
Val 570 | Ala 570 | variant |
Gly 614 | Asp 614 | variant |
Ser 621 | Pro 621 | variant |
Tyr 655 | His 655 | variant |
Val 670 | Ile 670 | variant |
Lys 679 | Asn 679 | variant |
Arg 681 | Pro 681 | variant |
Lys 764 | Asn 764 | variant |
Tyr 796 | Asp 796 | variant |
Pro 817 | Phe 817 | engineered mutation |
Pro 892 | Ala 892 | engineered mutation |
Pro 899 | Ala 899 | engineered mutation |
Phe 939 | Ser 939 | variant |
Pro 942 | Ala 942 | engineered mutation |
His 954 | Gln 954 | variant |
Lys 969 | Asn 969 | variant |
Pro 986 | Lys 986 | engineered mutation |
Pro 987 | Val 987 | engineered mutation |
Leu 1143 | Pro 1143 | variant |
Gly 1209 | - | expression tag |
Gly 1210 | - | expression tag |
Gly 1211 | - | expression tag |
Ser 1212 | - | expression tag |
Gly 1213 | - | expression tag |
Tyr 1214 | - | expression tag |
Ile 1215 | - | expression tag |
Pro 1216 | - | expression tag |
Glu 1217 | - | expression tag |
Ala 1218 | - | expression tag |
Pro 1219 | - | expression tag |
Arg 1220 | - | expression tag |
Asp 1221 | - | expression tag |
Gly 1222 | - | expression tag |
Gln 1223 | - | expression tag |
Ala 1224 | - | expression tag |
Tyr 1225 | - | expression tag |
Val 1226 | - | expression tag |
Arg 1227 | - | expression tag |
Lys 1228 | - | expression tag |
Asp 1229 | - | expression tag |
Gly 1230 | - | expression tag |
Glu 1231 | - | expression tag |
Trp 1232 | - | expression tag |
Val 1233 | - | expression tag |
Leu 1234 | - | expression tag |
Leu 1235 | - | expression tag |
Ser 1236 | - | expression tag |
Thr 1237 | - | expression tag |
Phe 1238 | - | expression tag |
Leu 1239 | - | expression tag |
Gly 1240 | - | expression tag |
Gly 1241 | - | expression tag |
Gly 1242 | - | expression tag |
Ser 1243 | - | expression tag |
Ala 1244 | - | expression tag |
Trp 1245 | - | expression tag |
Ser 1246 | - | expression tag |
His 1247 | - | expression tag |
Pro 1248 | - | expression tag |
Gln 1249 | - | expression tag |
Phe 1250 | - | expression tag |
Glu 1251 | - | expression tag |
Lys 1252 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
Polymers | Number of chains | 2 |
Total formula weight | 208679.7 | |
Branched | Number of molecules | 5 |
Total formula weight | 2446.3 | |
Non-Polymers* | Number of molecules | 4 |
Total formula weight | 729.0 | |
All* | Total formula weight | 211855.0 |